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tripal
Stephen Ficklin 9bd14e2dfa Fixed some formatting issues with some templates. Fixed update_hook_N numbers. Fixed a problem with taxonomy terms being re-assigned to a field_data_taxonomyextra table during upgrade of D6 to D7 %!s(int64=11) %!d(string=hai) anos
docs 8a898014b8 Renamed branch from 7.x-1.x to 7.x-2.x. Also merged bug fixes from 6.x-1.x %!s(int64=11) %!d(string=hai) anos
tripal_analysis 9bd14e2dfa Fixed some formatting issues with some templates. Fixed update_hook_N numbers. Fixed a problem with taxonomy terms being re-assigned to a field_data_taxonomyextra table during upgrade of D6 to D7 %!s(int64=11) %!d(string=hai) anos
tripal_bulk_loader 9bd14e2dfa Fixed some formatting issues with some templates. Fixed update_hook_N numbers. Fixed a problem with taxonomy terms being re-assigned to a field_data_taxonomyextra table during upgrade of D6 to D7 %!s(int64=11) %!d(string=hai) anos
tripal_contact 9bd14e2dfa Fixed some formatting issues with some templates. Fixed update_hook_N numbers. Fixed a problem with taxonomy terms being re-assigned to a field_data_taxonomyextra table during upgrade of D6 to D7 %!s(int64=11) %!d(string=hai) anos
tripal_core 9bd14e2dfa Fixed some formatting issues with some templates. Fixed update_hook_N numbers. Fixed a problem with taxonomy terms being re-assigned to a field_data_taxonomyextra table during upgrade of D6 to D7 %!s(int64=11) %!d(string=hai) anos
tripal_cv 35ba7a5327 API: Updated db api to match new names -complete %!s(int64=11) %!d(string=hai) anos
tripal_db 35ba7a5327 API: Updated db api to match new names -complete %!s(int64=11) %!d(string=hai) anos
tripal_example 283f42f54c Fixed problem with hook_node_access functions denying all pages %!s(int64=11) %!d(string=hai) anos
tripal_feature 9bd14e2dfa Fixed some formatting issues with some templates. Fixed update_hook_N numbers. Fixed a problem with taxonomy terms being re-assigned to a field_data_taxonomyextra table during upgrade of D6 to D7 %!s(int64=11) %!d(string=hai) anos
tripal_featuremap 283f42f54c Fixed problem with hook_node_access functions denying all pages %!s(int64=11) %!d(string=hai) anos
tripal_genetic 6bd10c5a57 Fixed issues with ND genotypes/phenotypes templates for stocks %!s(int64=11) %!d(string=hai) anos
tripal_library 9bd14e2dfa Fixed some formatting issues with some templates. Fixed update_hook_N numbers. Fixed a problem with taxonomy terms being re-assigned to a field_data_taxonomyextra table during upgrade of D6 to D7 %!s(int64=11) %!d(string=hai) anos
tripal_natural_diversity 6bd10c5a57 Fixed issues with ND genotypes/phenotypes templates for stocks %!s(int64=11) %!d(string=hai) anos
tripal_organism 9bd14e2dfa Fixed some formatting issues with some templates. Fixed update_hook_N numbers. Fixed a problem with taxonomy terms being re-assigned to a field_data_taxonomyextra table during upgrade of D6 to D7 %!s(int64=11) %!d(string=hai) anos
tripal_phenotype a3faf9f7ef Views: Created a function to handle making default views compatible with external chado instances by removing non-chado tables from the definition and implemented it for all chado default views. %!s(int64=11) %!d(string=hai) anos
tripal_project 9bd14e2dfa Fixed some formatting issues with some templates. Fixed update_hook_N numbers. Fixed a problem with taxonomy terms being re-assigned to a field_data_taxonomyextra table during upgrade of D6 to D7 %!s(int64=11) %!d(string=hai) anos
tripal_pub 9bd14e2dfa Fixed some formatting issues with some templates. Fixed update_hook_N numbers. Fixed a problem with taxonomy terms being re-assigned to a field_data_taxonomyextra table during upgrade of D6 to D7 %!s(int64=11) %!d(string=hai) anos
tripal_stock 9bd14e2dfa Fixed some formatting issues with some templates. Fixed update_hook_N numbers. Fixed a problem with taxonomy terms being re-assigned to a field_data_taxonomyextra table during upgrade of D6 to D7 %!s(int64=11) %!d(string=hai) anos
tripal_views 9bd14e2dfa Fixed some formatting issues with some templates. Fixed update_hook_N numbers. Fixed a problem with taxonomy terms being re-assigned to a field_data_taxonomyextra table during upgrade of D6 to D7 %!s(int64=11) %!d(string=hai) anos
.gitignore 455df59fcc removing empty lines %!s(int64=13) %!d(string=hai) anos
LICENSE.txt f8f44afa9c Added orphaned form items to sync form. Library module is now converted. %!s(int64=11) %!d(string=hai) anos
README.txt 8a898014b8 Renamed branch from 7.x-1.x to 7.x-2.x. Also merged bug fixes from 6.x-1.x %!s(int64=11) %!d(string=hai) anos

README.txt

What is Tripal?
--------------
Tripal is a collection of open-source freely available Drupal modules
and is a member of the GMOD family of tools. Tripal serves as a web
interface for the GMOD Chado database and is designed to allow anyone
with genomic data to quickly create an online genomic database using
community supported tools.


Features
--------------
- a Chado installer
- Data loaders for ontologies (controlled vocabularies), GFF files,
and FASTA files
- Generic Data Loader Modules allows for creation of custom loading
templates
- Drupal nodes (web pages) are automatically generated for organisms,
genomic features, biological libraries, and stocks
- Web pages can be enriched with analysis results from BLAST,
KAAS/KEGG, InterProScan, and Gene Ontology (GO)
- Views Integration allows for custom listings of data
- Content pieces exposed as blocks allowing the use of Panels for
custom layouts of Tripal Nodes


Required Modules
--------------
- Drupal 6.x (work is currently underway for a 7.x compatible
version)
- Drupal Core Modules: Search and Path
- Database containing GMOD Chado Schema (can be installed by the
Tripal Core module)
NOTE: A PostgreSQL database is required for installation of the
Chado Schema

Highly Recommended Modules
- Views 2.x (Views 3.x compatible version already exists in 6.x-0.4-dev)
- Views Data Export


Installation
--------------
Please follow the online tutorial for installation instructions:
http://www.gmod.org/wiki/Tripal_Tutorial_v1.1


Customization
--------------
Tripal can be used “as is” but also allows for complete customization.
PHP-based template files are provided for all data types to allow for
precise customizations as required by the community. A well-developed
Tripal API provides a uniform set of variables and functions for
accessing any and all data within the Chado database.


Future Work
--------------
Currently, Tripal only supports a large subset of the
current Chado schema, but further development is underway. Meanwhile,
others can use the Tripal API to develop their own extensions. Those
extensions can in turn be made available for anyone to use. These
custom extensions, the Tripal package, and access to support resource
such as an active mailing list can be found on the Tripal website
(http://tripal.sourceforge.net).

For more information, see the recent publication:

Stephen P. Ficklin, Lacey-Anne Sanderson, Chun-Huai Cheng, Margaret
Staton, Taein Lee, Il-Hyung Cho, Sook Jung, Kirstin E Bett, Dorrie
Main. Tripal: a construction Toolkit for Online Genome Databases.
Database, Sept 2011. Vol 2011.